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EC Number

Catalytic Site Atlas

CSA LITERATURE entry for 1ush

E.C. name5'-nucleotidase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1ush1ho5,1hp1,1hpu,1oi8,1oid,1oie,2ush,2z1a,
CSA Entries With UniProtID P07024
CSA Entries With EC Number
PDBe Entry 1ush
PDBSum Entry 1ush
MACiE Entry 1ush

Literature Report

Introduction5'-nucleotidase is a zinc-containing enzyme involved in ATP hydrolysis and is bound to the membrane as an extracellular nucleotidase, or ectonucleotidase. Bacterial 5'-nucleotidases show a significant sequence homology to animal counterparts suggesting a common evolutionary origin. It is also related to 2',3'-cyclic phosphodiesterases and apyrases, all being part of the superfamily of metallophosphoesterases which also includes the Ser/Thr protein phosphatases and the purple acid phosphatases. The enzyme also has a UDP-sugar hydrolase activity which catalyses the periplasmic degradation of external UDP-glucose to uridine, glucose-1-phosphate and phosphate.
Mechansim5'-nucleotidase catalyses the hydrolytic cleavage of 5'-mononucleotides to nucleoside and phosphate by nucleophilic attack of a water molecule on the phosphorous. A water ligand is coordinated to the di-zinc centre. The phosphate group of the substrate binds with one oxygen atom to a metal ion. The metal-bound water attacks the phosphorous nucleophilically, with the proton transferred to His 117. The pentahedral transition state is stabilised by both metal ions, Asn 116, Arg 375, Arg 379, Arg 410 and His 117. After expulsion of the leaving group the tetrahedral phosphate ion remains bound to the dimetal centre.

Catalytic Sites for 1ush

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA375375macie:sideChainContributes to positive potential at the active site and stabilise transition state.
AspA120120macie:sideChainActivates the His 117 to allow it to act as a general base.
ArgA410410macie:sideChainContributes to the distinct positive potential at the active site and stabilises the pentacoordinate transition state.
HisA117117macie:sideChainFacilitates proton transfer from water and acts to stabilise the pentacoordinate transition state.
ArgA379379macie:sideChainContributes to the distinct positive potential at the active site and stabilises the pentacoordinate transition state.
AsnA116116macie:sideChainStabilises the pentacoordinate transition state.

Literature References

Knöfel T
X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site.
Nat Struct Biol 1999 6 448-453
PubMed: 10331872
Knöfel T
Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
J Mol Biol 2001 309 239-254
PubMed: 11491293